[2024-01-24 11:43:25,071] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:25,075] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:25,075] [INFO] DQC Reference Directory: /var/lib/cwl/stg6bd11a2c-a662-4bdd-a49b-f2fd883478c4/dqc_reference
[2024-01-24 11:43:30,056] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:30,057] [INFO] Task started: Prodigal
[2024-01-24 11:43:30,057] [INFO] Running command: gunzip -c /var/lib/cwl/stgfbe39780-1e7f-4d2b-b35c-676be1804400/GCF_013388295.1_ASM1338829v1_genomic.fna.gz | prodigal -d GCF_013388295.1_ASM1338829v1_genomic.fna/cds.fna -a GCF_013388295.1_ASM1338829v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:33,765] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:33,765] [INFO] Task started: HMMsearch
[2024-01-24 11:43:33,765] [INFO] Running command: hmmsearch --tblout GCF_013388295.1_ASM1338829v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6bd11a2c-a662-4bdd-a49b-f2fd883478c4/dqc_reference/reference_markers.hmm GCF_013388295.1_ASM1338829v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:34,002] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:34,003] [INFO] Found 6/6 markers.
[2024-01-24 11:43:34,034] [INFO] Query marker FASTA was written to GCF_013388295.1_ASM1338829v1_genomic.fna/markers.fasta
[2024-01-24 11:43:34,034] [INFO] Task started: Blastn
[2024-01-24 11:43:34,034] [INFO] Running command: blastn -query GCF_013388295.1_ASM1338829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bd11a2c-a662-4bdd-a49b-f2fd883478c4/dqc_reference/reference_markers.fasta -out GCF_013388295.1_ASM1338829v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:35,013] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:35,017] [INFO] Selected 16 target genomes.
[2024-01-24 11:43:35,017] [INFO] Target genome list was writen to GCF_013388295.1_ASM1338829v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:35,033] [INFO] Task started: fastANI
[2024-01-24 11:43:35,034] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbe39780-1e7f-4d2b-b35c-676be1804400/GCF_013388295.1_ASM1338829v1_genomic.fna.gz --refList GCF_013388295.1_ASM1338829v1_genomic.fna/target_genomes.txt --output GCF_013388295.1_ASM1338829v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:41,489] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:41,490] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6bd11a2c-a662-4bdd-a49b-f2fd883478c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:41,490] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6bd11a2c-a662-4bdd-a49b-f2fd883478c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:41,503] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:43:41,504] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:43:41,504] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Bartonella alsatica	strain=CIP 105477	GCA_013388295.1	52764	52764	type	True	100.0	552	553	95	conclusive
Bartonella alsatica	strain=IBS 382	GCA_000280015.1	52764	52764	type	True	99.9602	548	553	95	conclusive
Bartonella callosciuri	strain=DSM 28538	GCA_014203215.1	686223	686223	type	True	84.8541	471	553	95	below_threshold
Bartonella florencae	strain=R4	GCA_000312525.1	928210	928210	type	True	84.8058	466	553	95	below_threshold
Bartonella phoceensis	strain=CIP107707	GCA_902825145.1	270249	270249	type	True	84.7971	467	553	95	below_threshold
Bartonella birtlesii	strain=IBS 325	GCA_000273375.1	111504	111504	type	True	84.7933	466	553	95	below_threshold
Bartonella vinsonii subsp. arupensis	strain=ATCC 700727	GCA_902825115.1	110578	33047	type	True	84.604	463	553	95	below_threshold
Bartonella vinsonii subsp. berkhoffii	strain=ATCC 51672	GCA_000518105.1	40933	33047	type	True	84.5764	463	553	95	below_threshold
Bartonella vinsonii subsp. arupensis	strain=OK-94-513	GCA_000278235.1	110578	33047	type	True	84.5567	458	553	95	below_threshold
Bartonella vinsonii subsp. berkhoffii	strain=CIP 104960	GCA_902825225.1	40933	33047	type	True	84.5117	460	553	95	below_threshold
Bartonella henselae	strain=Houston-I	GCA_002735245.1	38323	38323	type	True	84.4066	470	553	95	below_threshold
Bartonella henselae	strain=FDAARGOS_1462	GCA_019930925.1	38323	38323	type	True	84.3139	481	553	95	below_threshold
Bartonella henselae	strain=G-5436	GCA_021560445.1	38323	38323	type	True	84.2792	479	553	95	below_threshold
Bartonella koehlerae subsp. koehlerae	strain=C-29	GCA_000706625.1	1819240	92181	type	True	84.0271	466	553	95	below_threshold
Bartonella harrusi	strain=117A	GCA_024297065.1	2961895	2961895	type	True	83.5823	463	553	95	below_threshold
Bartonella krasnovii	strain=OE 1-1	GCA_003606345.3	2267275	2267275	type	True	82.1521	475	553	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:41,506] [INFO] DFAST Taxonomy check result was written to GCF_013388295.1_ASM1338829v1_genomic.fna/tc_result.tsv
[2024-01-24 11:43:41,506] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:41,506] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:41,507] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6bd11a2c-a662-4bdd-a49b-f2fd883478c4/dqc_reference/checkm_data
[2024-01-24 11:43:41,508] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:41,526] [INFO] Task started: CheckM
[2024-01-24 11:43:41,526] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013388295.1_ASM1338829v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013388295.1_ASM1338829v1_genomic.fna/checkm_input GCF_013388295.1_ASM1338829v1_genomic.fna/checkm_result
[2024-01-24 11:43:59,792] [INFO] Task succeeded: CheckM
[2024-01-24 11:43:59,793] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:43:59,811] [INFO] ===== Completeness check finished =====
[2024-01-24 11:43:59,812] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:43:59,813] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013388295.1_ASM1338829v1_genomic.fna/markers.fasta)
[2024-01-24 11:43:59,813] [INFO] Task started: Blastn
[2024-01-24 11:43:59,813] [INFO] Running command: blastn -query GCF_013388295.1_ASM1338829v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bd11a2c-a662-4bdd-a49b-f2fd883478c4/dqc_reference/reference_markers_gtdb.fasta -out GCF_013388295.1_ASM1338829v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:00,604] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:00,608] [INFO] Selected 14 target genomes.
[2024-01-24 11:44:00,608] [INFO] Target genome list was writen to GCF_013388295.1_ASM1338829v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:00,617] [INFO] Task started: fastANI
[2024-01-24 11:44:00,618] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbe39780-1e7f-4d2b-b35c-676be1804400/GCF_013388295.1_ASM1338829v1_genomic.fna.gz --refList GCF_013388295.1_ASM1338829v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013388295.1_ASM1338829v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:06,476] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:06,488] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:06,488] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_013388295.1	s__Bartonella alsatica	100.0	553	553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.98	99.96	0.99	0.99	3	conclusive
GCF_000278295.1	s__Bartonella taylorii	85.3929	492	553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	98.74	97.76	0.94	0.92	5	-
GCF_902825155.1	s__Bartonella taylorii_A	85.3452	467	553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000278115.1	s__Bartonella sp000278115	85.0729	482	553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	97.72	97.72	0.97	0.97	2	-
GCF_014203215.1	s__Bartonella callosciuri	84.8484	472	553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902825145.1	s__Bartonella phoceensis	84.7971	467	553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000312525.1	s__Bartonella florencae	84.7837	467	553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000273375.1	s__Bartonella birtlesii	84.7124	467	553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.71	99.25	0.98	0.95	6	-
GCF_000278235.1	s__Bartonella arupensis	84.5401	459	553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.53	99.17	0.97	0.95	3	-
GCF_902825225.1	s__Bartonella berkhoffii	84.4682	462	553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.74	99.27	0.97	0.95	4	-
GCF_000046705.1	s__Bartonella henselae	84.3525	472	553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.52	98.81	0.98	0.94	29	-
GCF_000278135.1	s__Bartonella washoeensis	84.3421	473	553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	98.94	98.02	0.92	0.91	3	-
GCF_009936175.1	s__Bartonella quintana	84.2259	449	553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	98.46	98.37	0.99	0.97	18	-
GCF_000706625.1	s__Bartonella koehlerae	84.0381	465	553	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Bartonella	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:06,490] [INFO] GTDB search result was written to GCF_013388295.1_ASM1338829v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:06,490] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:06,494] [INFO] DFAST_QC result json was written to GCF_013388295.1_ASM1338829v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:06,494] [INFO] DFAST_QC completed!
[2024-01-24 11:44:06,494] [INFO] Total running time: 0h0m41s